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WP9: From cells to molecules: integrating structural data

This initiative, commencing in January 2013, aims to foster a bilateral collaboration between Instruct and Elixir, focusing on integrating structural data across various platforms. Immediate objectives include surveying available software, investigating the inclusion of non-deposited information, and enhancing participation from various research infrastructures, including BioMedBridges. Key tasks involve the annotation of segmented volume data and describing conformational variability, adhering to EBI norms. The project will evaluate metrics such as accuracy in shape matching and software usage across the Instruct community.

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WP9: From cells to molecules: integrating structural data

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  1. WP9: From cells to molecules: integrating structural data Martyn Winn - STFC, Instruct Gerard Kleywegt - EBI, Elixir Lucia Banci - CERM, Instruct Ardan Patwardhan - EBI, Elixir Narayanan Krishnan - STFC, Instruct (WP4) Larry Hunter (SAB)

  2. Plans • Due to start in Jan 2013 • Bilateral interaction between Instruct and Elixir • EBI and CERM have people, STFC needs to recruit • Immediate objectives: • survey available software • investigate how to include non-deposited information • Pull in more people from Instruct, Elixir - maybe other RIs

  3. BioMedBridges context • Task 2 deals with annotation of segmented volume data - WP3 could advise on annotation • Connection to EuroBioImaging? AIM. • Task 3 requires a description of conformational variability (flexibility, IDPs) - WP3 • WP4 - services will follow EBI norms • WP5 - no known issues • doesn't use personal data • data is generally in the public domain, pharma could use stand-alone version • software needs licensing

  4. Metrics • Metrics: • Accuracy of shape matching - test with known cases • Usage of software distributed within Instruct (e.g. via CCP-EM, CCP4) • Usage of web services • Evidence of usage by other RIs

  5. Feedback (added later) • AIM also 3D • look at nucleic acids, ligands • link to EuroBioImaging, report on correlative microscopy soon?

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